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Structure of the delta dII IRES eIF2-containing 48S initiation complex, closed conformation. Structure 12(delta dII).

Electron Microscopy
3.5Å resolution
PDB entry 7sys coloured by chain, front view.
PDB entry 7sys coloured by chain, side view.
PDB entry 7sys coloured by chain, top view.
Source organisms:
Assembly composition:
hetero 39-mer (preferred)
Entry contents: 36 distinct polypeptide molecules
3 distinct RNA molecules

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Assemblies

Assembly 1 (preferred)
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Multimeric state: hetero 39-mer
Accessible surface area: 470282.93 Å2
Buried surface area: 202794.62 Å2
Dissociation area: 1,724.08 Å2
Dissociation energy (ΔGdiss): -3.17 kcal/mol
Dissociation entropy (TΔSdiss): 12.55 kcal/mol
Symmetry number: 1
PDBe Complex ID: PDB-CPX-239221

Macromolecules

Eukaryotic translation initiation factor 1A, X-chromosomal
Chain: A
Length: 144 amino acids
Theoretical weight: 16.49 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P47813 (Residues: 1-144; Coverage: 100%)
Gene names: EIF1A, EIF1AX, EIF4C
Pfam: Translation initiation factor 1A / IF-1
InterPro:
Eukaryotic translation initiation factor 1A, X-chromosomal in PDB entry 7sys, assembly 1, front view.
Eukaryotic translation initiation factor 1A, X-chromosomal in PDB entry 7sys, assembly 1, side view.
Eukaryotic translation initiation factor 1A, X-chromosomal in PDB entry 7sys, assembly 1, top view.
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Small ribosomal subunit protein uS2
Chain: B
Length: 295 amino acids
Theoretical weight: 32.96 KDa
Source organism: Oryctolagus cuniculus
UniProt:
  • Canonical: G1TLT8 (Residues: 1-295; Coverage: 100%)
Gene name: RPSA
Pfam:
InterPro:
Small ribosomal subunit protein uS2 in PDB entry 7sys, assembly 1, front view.
Small ribosomal subunit protein uS2 in PDB entry 7sys, assembly 1, side view.
Small ribosomal subunit protein uS2 in PDB entry 7sys, assembly 1, top view.
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Small ribosomal subunit protein eS1
Chain: C
Length: 264 amino acids
Theoretical weight: 30 KDa
Source organism: Oryctolagus cuniculus
UniProt:
  • Canonical: G1SS70 (Residues: 1-264; Coverage: 100%)
Gene name: RPS3A
Pfam: Ribosomal S3Ae family
InterPro:
Small ribosomal subunit protein eS1 in PDB entry 7sys, assembly 1, front view.
Small ribosomal subunit protein eS1 in PDB entry 7sys, assembly 1, side view.
Small ribosomal subunit protein eS1 in PDB entry 7sys, assembly 1, top view.
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Large ribosomal subunit protein uL30
Chain: D
Length: 221 amino acids
Theoretical weight: 24.44 KDa
Source organism: Oryctolagus cuniculus
UniProt:
  • Canonical: G1SV32 (Residues: 155-192; Coverage: 18%)
Gene name: RPL7
InterPro:
Small ribosomal subunit protein uS5 in PDB entry 7sys, assembly 1, front view.
Small ribosomal subunit protein uS5 in PDB entry 7sys, assembly 1, side view.
Small ribosomal subunit protein uS5 in PDB entry 7sys, assembly 1, top view.
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Small ribosomal subunit protein uS3
Chain: E
Length: 281 amino acids
Theoretical weight: 31.15 KDa
Source organism: Oryctolagus cuniculus
UniProt:
  • Canonical: G1TNM3 (Residues: 1-243; Coverage: 100%)
Gene name: RPS3
Pfam:
InterPro:
Small ribosomal subunit protein uS3 in PDB entry 7sys, assembly 1, front view.
Small ribosomal subunit protein uS3 in PDB entry 7sys, assembly 1, side view.
Small ribosomal subunit protein uS3 in PDB entry 7sys, assembly 1, top view.
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40S ribosomal protein S4
Chain: F
Length: 263 amino acids
Theoretical weight: 29.65 KDa
Source organism: Oryctolagus cuniculus
UniProt:
  • Canonical: G1TA47 (Residues: 1-263; Coverage: 100%)
Pfam:
InterPro:
40S ribosomal protein S4 in PDB entry 7sys, assembly 1, front view.
40S ribosomal protein S4 in PDB entry 7sys, assembly 1, side view.
40S ribosomal protein S4 in PDB entry 7sys, assembly 1, top view.
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Small ribosomal subunit protein uS7
Chain: G
Length: 204 amino acids
Theoretical weight: 22.91 KDa
Source organism: Oryctolagus cuniculus
UniProt:
  • Canonical: G1TFM5 (Residues: 1-204; Coverage: 100%)
Gene name: RPS5
Pfam: Ribosomal protein S7p/S5e
InterPro:
Small ribosomal subunit protein uS7 domain-containing protein in PDB entry 7sys, assembly 1, front view.
Small ribosomal subunit protein uS7 domain-containing protein in PDB entry 7sys, assembly 1, side view.
Small ribosomal subunit protein uS7 domain-containing protein in PDB entry 7sys, assembly 1, top view.
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40S ribosomal protein S6
Chain: H
Length: 249 amino acids
Theoretical weight: 28.75 KDa
Source organism: Oryctolagus cuniculus
UniProt:
  • Canonical: A0A5K1UJS7 (Residues: 1-249; Coverage: 100%)
Pfam: Ribosomal protein S6e
InterPro:
40S ribosomal protein S6 in PDB entry 7sys, assembly 1, front view.
40S ribosomal protein S6 in PDB entry 7sys, assembly 1, side view.
40S ribosomal protein S6 in PDB entry 7sys, assembly 1, top view.
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Small ribosomal subunit protein eS7
Chain: I
Length: 432 amino acids
Theoretical weight: 47.36 KDa
Source organism: Oryctolagus cuniculus
UniProt:
  • Canonical: G1SVB0 (Residues: 1-194; Coverage: 100%)
Gene name: RPS7
InterPro:
Small ribosomal subunit protein eS7 in PDB entry 7sys, assembly 1, front view.
Small ribosomal subunit protein eS7 in PDB entry 7sys, assembly 1, side view.
Small ribosomal subunit protein eS7 in PDB entry 7sys, assembly 1, top view.
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Small ribosomal subunit protein eS8
Chain: J
Length: 208 amino acids
Theoretical weight: 24.26 KDa
Source organism: Oryctolagus cuniculus
UniProt:
  • Canonical: G1TJW1 (Residues: 1-208; Coverage: 100%)
Gene name: RPS8
Pfam: Ribosomal protein S8e
InterPro:
40S ribosomal protein S8 in PDB entry 7sys, assembly 1, front view.
40S ribosomal protein S8 in PDB entry 7sys, assembly 1, side view.
40S ribosomal protein S8 in PDB entry 7sys, assembly 1, top view.
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Small ribosomal subunit protein uS4
Chain: K
Length: 194 amino acids
Theoretical weight: 22.64 KDa
Source organism: Oryctolagus cuniculus
UniProt:
  • Canonical: B7NZS8 (Residues: 1-194; Coverage: 100%)
Gene name: RPS9
Pfam:
InterPro:
Small ribosomal subunit protein uS4 in PDB entry 7sys, assembly 1, front view.
Small ribosomal subunit protein uS4 in PDB entry 7sys, assembly 1, side view.
Small ribosomal subunit protein uS4 in PDB entry 7sys, assembly 1, top view.
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Small ribosomal subunit protein eS10
Chain: L
Length: 149 amino acids
Theoretical weight: 17.16 KDa
Source organism: Oryctolagus cuniculus
UniProt:
  • Canonical: G1TPV3 (Residues: 1-149; Coverage: 90%)
Pfam: Plectin/S10 domain
InterPro:
Plectin/eS10 N-terminal domain-containing protein in PDB entry 7sys, assembly 1, front view.
Plectin/eS10 N-terminal domain-containing protein in PDB entry 7sys, assembly 1, side view.
Plectin/eS10 N-terminal domain-containing protein in PDB entry 7sys, assembly 1, top view.
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Small ribosomal subunit protein uS17
Chain: M
Length: 158 amino acids
Theoretical weight: 18.47 KDa
Source organism: Oryctolagus cuniculus
UniProt:
  • Canonical: G1TRM4 (Residues: 1-158; Coverage: 100%)
Gene name: RPS11
Pfam:
InterPro:
Small ribosomal subunit protein uS17 in PDB entry 7sys, assembly 1, front view.
Small ribosomal subunit protein uS17 in PDB entry 7sys, assembly 1, side view.
Small ribosomal subunit protein uS17 in PDB entry 7sys, assembly 1, top view.
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Small ribosomal subunit protein eS12
Chain: N
Length: 132 amino acids
Theoretical weight: 14.54 KDa
Source organism: Oryctolagus cuniculus
UniProt:
  • Canonical: G1SFR8 (Residues: 1-132; Coverage: 100%)
Gene name: RPS12
Pfam: Ribosomal protein L7Ae/L30e/S12e/Gadd45 family
InterPro:
40S ribosomal protein S12 in PDB entry 7sys, assembly 1, front view.
40S ribosomal protein S12 in PDB entry 7sys, assembly 1, side view.
40S ribosomal protein S12 in PDB entry 7sys, assembly 1, top view.
Molecule details ›

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Small ribosomal subunit protein uS15
Chain: O
Length: 151 amino acids
Theoretical weight: 17.26 KDa
Source organism: Oryctolagus cuniculus
UniProt:
  • Canonical: G1SP51 (Residues: 1-151; Coverage: 100%)
Gene name: RPS13
Pfam:
InterPro:
Small ribosomal subunit protein uS15 in PDB entry 7sys, assembly 1, front view.
Small ribosomal subunit protein uS15 in PDB entry 7sys, assembly 1, side view.
Small ribosomal subunit protein uS15 in PDB entry 7sys, assembly 1, top view.
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Small ribosomal subunit protein uS11
Chain: P
Length: 168 amino acids
Theoretical weight: 18.13 KDa
Source organism: Oryctolagus cuniculus
UniProt:
  • Canonical: G1T1F0 (Residues: 1-151; Coverage: 100%)
Gene name: RPS14
Pfam: Ribosomal protein S11
InterPro:
Ribosomal protein S14 in PDB entry 7sys, assembly 1, front view.
Ribosomal protein S14 in PDB entry 7sys, assembly 1, side view.
Ribosomal protein S14 in PDB entry 7sys, assembly 1, top view.
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Small ribosomal subunit protein uS19
Chain: Q
Length: 145 amino acids
Theoretical weight: 17.05 KDa
Source organism: Oryctolagus cuniculus
UniProt:
  • Canonical: G1U0Q2 (Residues: 1-145; Coverage: 100%)
Gene name: RPS15
Pfam: Ribosomal protein S19
InterPro:
40S ribosomal protein S15 in PDB entry 7sys, assembly 1, front view.
40S ribosomal protein S15 in PDB entry 7sys, assembly 1, side view.
40S ribosomal protein S15 in PDB entry 7sys, assembly 1, top view.
Molecule details ›

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Small ribosomal subunit protein uS9
Chain: R
Length: 172 amino acids
Theoretical weight: 19.21 KDa
Source organism: Oryctolagus cuniculus
UniProt:
  • Canonical: G1SGX4 (Residues: 1-146; Coverage: 100%)
Gene name: RPS16
Pfam: Ribosomal protein S9/S16
InterPro:
Ribosomal protein S16 in PDB entry 7sys, assembly 1, front view.
Ribosomal protein S16 in PDB entry 7sys, assembly 1, side view.
Ribosomal protein S16 in PDB entry 7sys, assembly 1, top view.
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Small ribosomal subunit protein eS17
Chain: S
Length: 135 amino acids
Theoretical weight: 15.55 KDa
Source organism: Oryctolagus cuniculus
UniProt:
  • Canonical: G1TU13 (Residues: 1-135; Coverage: 100%)
Gene name: RPS17
Pfam: Ribosomal S17
InterPro:
Small ribosomal subunit protein eS17 in PDB entry 7sys, assembly 1, front view.
Small ribosomal subunit protein eS17 in PDB entry 7sys, assembly 1, side view.
Small ribosomal subunit protein eS17 in PDB entry 7sys, assembly 1, top view.
Molecule details ›

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Small ribosomal subunit protein uS13
Chain: T
Length: 152 amino acids
Theoretical weight: 17.76 KDa
Source organism: Oryctolagus cuniculus
UniProt:
  • Canonical: G1TPG3 (Residues: 1-152; Coverage: 100%)
Gene name: RPS18
Pfam: Ribosomal protein S13/S18
InterPro:
Small ribosomal subunit protein uS13 in PDB entry 7sys, assembly 1, front view.
Small ribosomal subunit protein uS13 in PDB entry 7sys, assembly 1, side view.
Small ribosomal subunit protein uS13 in PDB entry 7sys, assembly 1, top view.
Molecule details ›

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Small ribosomal subunit protein eS19
Chain: U
Length: 145 amino acids
Theoretical weight: 16.24 KDa
Source organism: Oryctolagus cuniculus
UniProt:
  • Canonical: G1TN62 (Residues: 1-145; Coverage: 100%)
Gene name: RPS19
Pfam: Ribosomal protein S19e
InterPro:
Small ribosomal subunit protein eS19 in PDB entry 7sys, assembly 1, front view.
Small ribosomal subunit protein eS19 in PDB entry 7sys, assembly 1, side view.
Small ribosomal subunit protein eS19 in PDB entry 7sys, assembly 1, top view.
Molecule details ›

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Small ribosomal subunit protein uS10
Chain: V
Length: 119 amino acids
Theoretical weight: 13.4 KDa
Source organism: Oryctolagus cuniculus
UniProt:
  • Canonical: G1SIZ2 (Residues: 1-119; Coverage: 100%)
Gene name: RPS20
Pfam: Ribosomal protein S10p/S20e
InterPro:
Small ribosomal subunit protein uS10 in PDB entry 7sys, assembly 1, front view.
Small ribosomal subunit protein uS10 in PDB entry 7sys, assembly 1, side view.
Small ribosomal subunit protein uS10 in PDB entry 7sys, assembly 1, top view.
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Small ribosomal subunit protein eS21
Chain: W
Length: 83 amino acids
Theoretical weight: 9.12 KDa
Source organism: Oryctolagus cuniculus
UniProt:
  • Canonical: G1TM82 (Residues: 1-83; Coverage: 100%)
Gene name: RPS21
Pfam: Ribosomal protein S21e
InterPro:
Small ribosomal subunit protein eS21 in PDB entry 7sys, assembly 1, front view.
Small ribosomal subunit protein eS21 in PDB entry 7sys, assembly 1, side view.
Small ribosomal subunit protein eS21 in PDB entry 7sys, assembly 1, top view.
Molecule details ›

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Small ribosomal subunit protein uS8
Chain: X
Length: 130 amino acids
Theoretical weight: 14.87 KDa
Source organism: Oryctolagus cuniculus
UniProt:
  • Canonical: G1TG89 (Residues: 1-130; Coverage: 100%)
Gene name: RPS15A
Pfam: Ribosomal protein S8
InterPro:
Small ribosomal subunit protein uS8 in PDB entry 7sys, assembly 1, front view.
Small ribosomal subunit protein uS8 in PDB entry 7sys, assembly 1, side view.
Small ribosomal subunit protein uS8 in PDB entry 7sys, assembly 1, top view.
Molecule details ›

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Small ribosomal subunit protein uS12
Chain: Y
Length: 143 amino acids
Theoretical weight: 15.84 KDa
Source organism: Oryctolagus cuniculus
UniProt:
  • Canonical: G1SZ47 (Residues: 1-143; Coverage: 100%)
Gene name: RPS23
Pfam: Ribosomal protein S12/S23
InterPro:
Small ribosomal subunit protein uS12 in PDB entry 7sys, assembly 1, front view.
Small ribosomal subunit protein uS12 in PDB entry 7sys, assembly 1, side view.
Small ribosomal subunit protein uS12 in PDB entry 7sys, assembly 1, top view.
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40S ribosomal protein S24
Chain: Z
Length: 131 amino acids
Theoretical weight: 15.24 KDa
Source organism: Oryctolagus cuniculus
UniProt:
  • Canonical: G1T3D8 (Residues: 1-131; Coverage: 100%)
Gene name: RPS24
Pfam: Ribosomal protein S24e
InterPro:
40S ribosomal protein S24 in PDB entry 7sys, assembly 1, front view.
40S ribosomal protein S24 in PDB entry 7sys, assembly 1, side view.
40S ribosomal protein S24 in PDB entry 7sys, assembly 1, top view.
Molecule details ›

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Small ribosomal subunit protein eS25
Chain: a
Length: 124 amino acids
Theoretical weight: 13.65 KDa
Source organism: Oryctolagus cuniculus
UniProt:
  • Canonical: G1TDB3 (Residues: 1-124; Coverage: 100%)
Gene name: RPS25
Pfam: S25 ribosomal protein
InterPro:
40S ribosomal protein S25 in PDB entry 7sys, assembly 1, front view.
40S ribosomal protein S25 in PDB entry 7sys, assembly 1, side view.
40S ribosomal protein S25 in PDB entry 7sys, assembly 1, top view.
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Small ribosomal subunit protein eS26
Chain: b
Length: 101 amino acids
Theoretical weight: 11.65 KDa
Source organism: Oryctolagus cuniculus
UniProt:
  • Canonical: G1TFE8 (Residues: 2-102; Coverage: 88%)
Gene name: RPS26
Pfam: Ribosomal protein S26e
InterPro:
40S ribosomal protein S26 in PDB entry 7sys, assembly 1, front view.
40S ribosomal protein S26 in PDB entry 7sys, assembly 1, side view.
40S ribosomal protein S26 in PDB entry 7sys, assembly 1, top view.
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Small ribosomal subunit protein eS27
Chain: c
Length: 84 amino acids
Theoretical weight: 9.48 KDa
Source organism: Oryctolagus cuniculus
UniProt:
  • Canonical: G1TZ76 (Residues: 1-84; Coverage: 100%)
Gene name: RPS27
Pfam: Ribosomal protein S27
InterPro:
40S ribosomal protein S27 in PDB entry 7sys, assembly 1, front view.
40S ribosomal protein S27 in PDB entry 7sys, assembly 1, side view.
40S ribosomal protein S27 in PDB entry 7sys, assembly 1, top view.
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Small ribosomal subunit protein eS28
Chain: d
Length: 69 amino acids
Theoretical weight: 7.86 KDa
Source organism: Oryctolagus cuniculus
UniProt:
  • Canonical: G1TIB4 (Residues: 1-69; Coverage: 100%)
Gene name: RPS28
Pfam: Ribosomal protein S28e
InterPro:
Small ribosomal subunit protein eS28 in PDB entry 7sys, assembly 1, front view.
Small ribosomal subunit protein eS28 in PDB entry 7sys, assembly 1, side view.
Small ribosomal subunit protein eS28 in PDB entry 7sys, assembly 1, top view.
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Small ribosomal subunit protein uS14
Chain: e
Length: 56 amino acids
Theoretical weight: 6.69 KDa
Source organism: Oryctolagus cuniculus
UniProt:
  • Canonical: G1U7M4 (Residues: 1-56; Coverage: 100%)
Gene name: RPS29
Pfam: Ribosomal protein S14p/S29e
InterPro:
Small ribosomal subunit protein uS14 in PDB entry 7sys, assembly 1, front view.
Small ribosomal subunit protein uS14 in PDB entry 7sys, assembly 1, side view.
Small ribosomal subunit protein uS14 in PDB entry 7sys, assembly 1, top view.
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Ubiquitin-like FUBI-ribosomal protein eS30 fusion protein
Chain: f
Length: 133 amino acids
Theoretical weight: 14.5 KDa
Source organism: Oryctolagus cuniculus
UniProt:
  • Canonical: G1T8A2 (Residues: 1-133; Coverage: 100%)
Gene name: FAU
Pfam:
InterPro:
Ubiquitin-like domain-containing protein in PDB entry 7sys, assembly 1, front view.
Ubiquitin-like domain-containing protein in PDB entry 7sys, assembly 1, side view.
Ubiquitin-like domain-containing protein in PDB entry 7sys, assembly 1, top view.
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Ubiquitin-ribosomal protein eS31 fusion protein
Chain: g
Length: 188 amino acids
Theoretical weight: 21.43 KDa
Source organism: Oryctolagus cuniculus
UniProt:
  • Canonical: G1SK22 (Residues: 18-156; Coverage: 89%)
Gene name: RPS27A
Pfam:
InterPro:
Ubiquitin-ribosomal protein eS31 fusion protein in PDB entry 7sys, assembly 1, front view.
Ubiquitin-ribosomal protein eS31 fusion protein in PDB entry 7sys, assembly 1, side view.
Ubiquitin-ribosomal protein eS31 fusion protein in PDB entry 7sys, assembly 1, top view.
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Small ribosomal subunit protein RACK1
Chain: h
Length: 317 amino acids
Theoretical weight: 35.12 KDa
Source organism: Oryctolagus cuniculus
UniProt:
  • Canonical: G1SJB4 (Residues: 1-317; Coverage: 100%)
Gene name: RACK1
Pfam: WD domain, G-beta repeat
InterPro:
Small ribosomal subunit protein RACK1 in PDB entry 7sys, assembly 1, front view.
Small ribosomal subunit protein RACK1 in PDB entry 7sys, assembly 1, side view.
Small ribosomal subunit protein RACK1 in PDB entry 7sys, assembly 1, top view.
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Eukaryotic translation initiation factor 2 subunit 1
Chain: j
Length: 315 amino acids
Theoretical weight: 36.16 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P05198 (Residues: 1-315; Coverage: 100%)
Gene names: EIF2A, EIF2S1
Pfam:
InterPro:
Eukaryotic translation initiation factor 2 subunit 1 in PDB entry 7sys, assembly 1, front view.
Eukaryotic translation initiation factor 2 subunit 1 in PDB entry 7sys, assembly 1, side view.
Eukaryotic translation initiation factor 2 subunit 1 in PDB entry 7sys, assembly 1, top view.
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Small ribosomal subunit protein eS32
Chain: n
Length: 25 amino acids
Theoretical weight: 3.47 KDa
Source organism: Oryctolagus cuniculus
UniProt:
  • Canonical: A0A087WNH4 (Residues: 1-25; Coverage: 100%)
Gene name: RPL41
Pfam: Ribosomal protein L41
InterPro: Large ribosomal subunit protein eS32
60S ribosomal protein L41 in PDB entry 7sys, assembly 1, front view.
60S ribosomal protein L41 in PDB entry 7sys, assembly 1, side view.
60S ribosomal protein L41 in PDB entry 7sys, assembly 1, top view.
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RNA chain 2
Name: 18S Ribosomal RNA
Representative chains: 2
Length: 1870 nucleotides
Theoretical weight: 603.1 KDa
Rfam: Eukaryotic small subunit ribosomal RNA
18S Ribosomal RNA in PDB entry 7sys, assembly 1, front view.
18S Ribosomal RNA in PDB entry 7sys, assembly 1, side view.
18S Ribosomal RNA in PDB entry 7sys, assembly 1, top view.
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RNA chain z
Name: HCV IRES
Representative chains: z
Length: 400 nucleotides
Theoretical weight: 128.75 KDa
Rfam: Hepatitis C virus internal ribosome entry site
HCV IRES in PDB entry 7sys, assembly 1, front view.
HCV IRES in PDB entry 7sys, assembly 1, side view.
HCV IRES in PDB entry 7sys, assembly 1, top view.
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RNA chain i
Name: Met-tRNA-i-Met
Representative chains: i
Length: 75 nucleotides
Theoretical weight: 24.23 KDa
Rfam: tRNA
Met-tRNA-i-Met in PDB entry 7sys, assembly 1, front view.
Met-tRNA-i-Met in PDB entry 7sys, assembly 1, side view.
Met-tRNA-i-Met in PDB entry 7sys, assembly 1, top view.
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